9GLM | pdb_00009glm

Crystal Structure of UFC1 W145F

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	1.5M Ammonium sulfate; 0.1M Bis-Tris propane pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.95	α = 90
b = 46.95	β = 90
c = 143.9	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS PILATUS 200K		2024-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54187

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.79	35.97	99.93	0.03872	1	18.78	2		15997			18.26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.79	1.854	99.94		0.3525	0.829	2.62	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.79	35.97	15997	787	99.931	0.195	0.1924	0.2003	0.238	0.2429	18.932

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.259			-0.259		0.517

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.915
r_dihedral_angle_4_deg	15.153
r_dihedral_angle_3_deg	13.597
r_dihedral_angle_1_deg	6.407
r_lrange_it	5.07
r_lrange_other	4.985
r_scangle_it	3.582
r_scangle_other	3.58
r_scbond_it	2.233
r_scbond_other	2.232
r_mcangle_other	2.078
r_mcangle_it	2.077
r_angle_refined_deg	1.536
r_mcbond_it	1.452
r_mcbond_other	1.408
r_angle_other_deg	1.404
r_symmetry_nbd_refined	0.342
r_nbd_other	0.223
r_nbd_refined	0.216
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.125
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1319
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building